Data from: Genomics of parallel experimental evolution in Drosophila

What are the genomic foundations of adaptation in sexual populations? We
address this question using fitness-character and whole-genome sequence
data from 30 Drosophila laboratory populations. These 30 populations are
part of a nearly forty-year laboratory radiation featuring three selection
regimes, each shared by ten populations for up to 837 generations, with
moderately large effective population sizes. Each of three sets of ten
populations that shared a selection regime consist of five populations
that have long been maintained under that selection regime, paired with
five populations that had only recently been subjected to that selection
regime. We find a high degree of evolutionary parallelism in fitness
phenotypes when most-recent selection regimes are shared, as in previous
studies from our laboratory. We also find genomic parallelism with respect
to the frequencies of single-nucleotide polymorphisms, transposable
elements, insertions, and structural variants, which was expected.
Entirely unexpected was a high degree of parallelism for linkage
disequilibrium. The evolutionary genetic changes among these sexual
populations are rapid and genomically extensive. This pattern may be due
to segregating functional genetic variation that is abundantly maintained
genome-wide by selection, variation that responds immediately to changes
of selection regime.